This study investigates the impact of carbon dioxide (CO2) on the pore structure of coal during CO2 injection to understand the technical challenges associated with CO2 sequestration in depleted coal seam gas reservoirs. In an integrated approach, Micro-Computed Tomography (micro-CT) scanning, helium porosity and air permeability tests are performed on a coal sample prior to and after CO2 flooding experiments to identify both reversible and irreversible changes in cleat and fracture networks. The results indicate that irreversible changes contribute to a 43% reduction in effective porosity, which can be readily observed in the 3D model of the cleat and fracture networks constructed after CO2 flooding. At lower effective stresses, pore compressibility offsets the matrix swelling effect, resulting in improved permeability, which is beneficial for CO2 injection. Additionally, the analysis of borehole image logs of the study well reveals that most fractures and cleats terminate within coal intervals, with very few fractures extending into adjacent strata that are siltstone and fine sandstone with very low permeability.